Understanding the sensitivity of groundwater generation to climate in a mountain system is complicated by the tight coupling of snow dynamics to vegetation and topography. To address these feedbacks, we combine light detection and ranging (LiDAR)-derived snow observations with an integrated hydrologic model to quantify spatially and temporally distributed water fluxes across varying climate conditions in a Colorado River headwater basin. Results indicate that annual groundwater flow is an important and stable source of stream water. However, interflow decreases during drought as a function increased plant water use and the relative fraction of groundwater to streams increases. Seasonal snowmelt and vegetation water use regulate small recharge rates in the lower portions of the basin, but snowmelt transported via interflow from high mountain ridges toward convergent topographic zones defines preferential recharge in the upper subalpine. Recharge in this zone appears decoupled from annual climate variability and resilient to drought.